So the cladist assigns individuals numbers and then groups these numbers according to a cladistic analysis? I would think that referring to everything as a number would be confusing. When (a long time ago) I used cladistics we retained the naming system. The numerical taxonomist still used the binomial naming system. There was then some discussion about the methods, and deciding at what level of branching was sufficient to elevate a group to the next taxonomic level. Some discussion of parsimony, and we moved on. If the numerical taxonomists have changed over to designating individuals by numbers I have not seen that in the literature (yet?). While I can see referring to Aphis gossypii as 437856429753024-432, I would think that would (in general) make it harder for people to relate and discuss the topic. People have enough trouble with Aphis gossylii, and we get common names (melon aphid, cotton aphid, brinjal aphid, etc...).

So I think I may still be missing something?

_____________________________

In terms of methods, I think that both ways need to be taught. The problem is that the system must be scientifically useful as well as useful for non-scientists. It may be that biology may go entirely molecular. However, our current tools are insufficient to accomplish the task. What is needed is to understand the gene space of all the organisms. This means that we need to routinely generate the entire gene sequence from individuals and that there exists a database wherein we know that "this gene sequence" is unique for the melon aphid while "that gene sequence" is for the green peach aphid. In this task we cannot rely on the gene sequence of one individual. We need thousands for each species. I don't see that happening in my lifetime. However, even if that were possible we would need to relate that to "that bug that I found under a leaf" or that flower, or mushroom, or bird. Unless we can get a genetic sequence at a distance there will be need and interest in identifying things the old fashioned way. If we lose the skill to identify organisms using morphological characters we will lose the connection with most of the research that has taken place over the last hundred years or so. What do we do for the grower that sees his crop being destroyed by some multi-legged critter. This could describe an insect or a mite, and I need some way to go to the grower have him hand me an example of this critter and be able to tell him what it is in a few seconds. That way he has time to find, buy, and then apply whatever product is necessary to solve his problem. If I have to send the sample away to a lab and wait a few weeks for a result -- that is just too late. The crop is dead, the farmer bankrupt, and things get less pleasant from there.

   All that said, there is great advantage to the molecular techniques. It may be the only way to decide if Aphis gossypii is a dozen or more cryptic species, or one species with a remarkable host range. If it is one species then we might ask why this aphid has evolved the ability to survive on a broad host range while most aphids are more monophagous. So having a clear understanding of phylogenetic relationships is very important to understanding ecological relationships and understanding how the natural and man-made environments function.

Dear Ramzi,

I think you confuse two different things - taxonomy and nomenclature. Taxonomy is, briefly speaking, the science of describing, identifying and classifying living organisms. Indeed, the methods used in taxonomy have changed considerably and so have the concepts for classification, i.e., species concepts. Decades ago taxonomists purely relied on morphological characters, whereas today one may also incorporate molecular and phylogenetic data. Nomenclature, however, is independent of the classification itself. It is merely concerned with the rules that govern the naming of the organisms. The binominal Linnean nomenclature is the only one generally accepted (and valid!).

Best regards,

thomas

There is a good book on nomenclature (though I am sure there is something more recent that is good too).

"Principles of Systematic Zoology" by Ernst Mayr

You might also look at this web site: http://iczn.org/

Dear Thomas,

Thanks for your precious answer. Yes I agree with your statement. My meaning here is classification of living organisms, I've edited this question.

Best regards,

Ramzi

Dear Timothy,

Thanks for your contribution and for providing this internet link.

Best regards,

Ramzi

I reread the question, and I still think that Thomas did a good job of answering the question. Cladistics still gives a binomial classification scheme. The members of ranks (Order, Family, Tribe, Genus) may change and the approach used to place species in ranks may change, but the system remains.

How do you view Cladistics as non-rank based? Or can you figure out how I am using or defining ranks that is different from what you are asking?

Dear Timothy,

Thanks for your answer.

In fact, the Linnaean System is characterized by Seven Major Ranked Categories of Classification: Kingdom, Phylum, Class, Order, Family, Genus, Species. The phylogenetic approach classify organisms based on their evolutionary relationships and, unlike the Linnaean system, these organisms are not assigned to ranks: Cladistics do not use the following ranks that are used in the Linnaean system: genus, family, order, class, phylum and kingdom. For this reason I wrote the Linnaean system followed by “rank-based”.

Cheers

So the cladist assigns individuals numbers and then groups these numbers according to a cladistic analysis? I would think that referring to everything as a number would be confusing. When (a long time ago) I used cladistics we retained the naming system. The numerical taxonomist still used the binomial naming system. There was then some discussion about the methods, and deciding at what level of branching was sufficient to elevate a group to the next taxonomic level. Some discussion of parsimony, and we moved on. If the numerical taxonomists have changed over to designating individuals by numbers I have not seen that in the literature (yet?). While I can see referring to Aphis gossypii as 437856429753024-432, I would think that would (in general) make it harder for people to relate and discuss the topic. People have enough trouble with Aphis gossylii, and we get common names (melon aphid, cotton aphid, brinjal aphid, etc...).

So I think I may still be missing something?

_____________________________

In terms of methods, I think that both ways need to be taught. The problem is that the system must be scientifically useful as well as useful for non-scientists. It may be that biology may go entirely molecular. However, our current tools are insufficient to accomplish the task. What is needed is to understand the gene space of all the organisms. This means that we need to routinely generate the entire gene sequence from individuals and that there exists a database wherein we know that "this gene sequence" is unique for the melon aphid while "that gene sequence" is for the green peach aphid. In this task we cannot rely on the gene sequence of one individual. We need thousands for each species. I don't see that happening in my lifetime. However, even if that were possible we would need to relate that to "that bug that I found under a leaf" or that flower, or mushroom, or bird. Unless we can get a genetic sequence at a distance there will be need and interest in identifying things the old fashioned way. If we lose the skill to identify organisms using morphological characters we will lose the connection with most of the research that has taken place over the last hundred years or so. What do we do for the grower that sees his crop being destroyed by some multi-legged critter. This could describe an insect or a mite, and I need some way to go to the grower have him hand me an example of this critter and be able to tell him what it is in a few seconds. That way he has time to find, buy, and then apply whatever product is necessary to solve his problem. If I have to send the sample away to a lab and wait a few weeks for a result -- that is just too late. The crop is dead, the farmer bankrupt, and things get less pleasant from there.

   All that said, there is great advantage to the molecular techniques. It may be the only way to decide if Aphis gossypii is a dozen or more cryptic species, or one species with a remarkable host range. If it is one species then we might ask why this aphid has evolved the ability to survive on a broad host range while most aphids are more monophagous. So having a clear understanding of phylogenetic relationships is very important to understanding ecological relationships and understanding how the natural and man-made environments function.

Dear Ramzi

I am also fully agree with the definitions of Thomas. I like his answer so much.

regards,

Islam

Dear Timothy,

Many thanks for your high quality answer, I greatly appreciate it !! We are both entomologists and this is always true for classifying (or identifying) insects (whose the majory are plant pests) based on phylogenetic approach: now it is not possible to make insect classification without the exploitation of phylogenetic tools (cladistics,...) and also without following the Linnean approach, I strongly believe that these two approaches are still complementary in this context, but what about classification of the other living organisms (other than insects and mites)? May be the most suitable classification approach (or to follow combined approaches) would depend on the nature of the living organism we are considering.

Cheers

The problems are the same for all organisms (except possibly viruses). Go to any field or forest near you. Can you site identify all the plants and fungi? I almost got to the point where I could site ID most of the plants in a small area in California. Then I had to move. Now I know a few of the agriculture weeds, and that is about it Yes, I can still tell an oak from a pine, but I can't tell which oak. I would be very nervous if I had to go to the forest and find 12 edible mushrooms, and eat them. I might survive. I would have given myself a better chance of success right after my systematic mycology course ... but 20+ years later and some 2000 miles away is another matter.

The least diverse group are the vertebrates. So if I give you a random frog, turtle,  or salamander from your area would you be able to name it? Would you have the resources to send off a small tissue sample (properly preserved) for identification? Would it be ethical to take such a sample, or would you have to kill the animal to get the sample? I would assume that you personally would be able to get the sample, but now consider your car mechanic, or the person who installed your cable TV. Would she know? Where would she learn? A half hour unit as part of a basic biology course in high school?

The closest thing we have to a numerical system of classification is that for the viruses. I am not really familiar with the system so I will leave it at this.

Bacteria, tardigrades, water fleas, fairy shrimp, sponges (fresh water, and salt), algae, diatoms, sea urchin larvae in the plankton, are all described and pictured in a vast assortment of arcane tomes. It is how people see and study the biological world about us. At least with current technology we are very much stuck with this system.

So I find an insect and I identify it as a melon aphid. I send it off to an expert and they agree that it is a melon aphid. My friend Arnold from Ghana also finds an aphid, and identifies it as a melon aphid. They look the same, and both perfectly key out as a melon aphid. For fun, we each sequence the entire genome of our aphid. There is 99% overlap. Are they really the same species? Does Arnold's aphid genome fit within the range of genome sequences present within all the melon aphids within North America?   These are important questions that we will be able to answer in time. However, the field of genetic biodiversity is not yet ready. The ability to quickly (